Overview of tsRNAsearch analysis comparing TotalRNA versus CytC_IP
Quantities of ncRNA features identified
Proportions of ncRNA groups identified (normalised by reads per million)
Number of raw reads identified for each ncRNA group
Venn diagram comparing the three methods used (DESeq2, distribution algorithm, cleavage algorithm)

Details of the intersections can be found here:
- /home/paul/Documents/Pipelines/tsRNAsearch/../Analyses_tsRNAsearch/Mouse-Hyperosmotic-stress-Angiogenin/Data/VennDiagramGeneration/TotalRNA_vs_CytC_IP.intersect…
Files used to generate the Venn Diagram can be found here:
- /home/paul/Documents/Pipelines/tsRNAsearch/../Analyses_tsRNAsearch/Mouse-Hyperosmotic-stress-Angiogenin/Data/VennDiagramGeneration
Summary Report Table
Top 20 results shown (sorted by distribution score)
| ENSMUSG00000093645 (Gm23187) |
0e+00 |
3802095.6 |
-4.650549 |
0.0000000 |
0.0000000 |
47934.615 |
| ENSMUSG00000065904 (Gm26109) |
0e+00 |
2922939.2 |
-4.038454 |
0.0000000 |
0.0000000 |
299509.758 |
| ENSMUSG00000080465 (Gm22486) |
0e+00 |
2618347.1 |
-2.493209 |
0.0000504 |
0.0002349 |
13435.727 |
| ENSMUSG00000088169 (Gm22059) |
0e+00 |
2055911.8 |
-7.053207 |
0.0000000 |
0.0000000 |
2225.282 |
| ENSMUSG00000095472 (Snord88a) |
0e+00 |
1710839.0 |
-5.086376 |
0.0000000 |
0.0000000 |
24166.419 |
| ENSMUSG00000065738 (Gm24494) |
1e-06 |
1194959.2 |
-3.701179 |
0.0000000 |
0.0000000 |
1430180.100 |
| ENSMUSG00000065628 (Snord33) |
0e+00 |
977968.5 |
-5.697055 |
0.0000000 |
0.0000000 |
261211.204 |
| ENSMUSG00000065735 (Snord80) |
0e+00 |
976233.4 |
-5.383236 |
0.0000000 |
0.0000000 |
466612.936 |
| ENSMUSG00000104627 (Mir3535) |
0e+00 |
892113.9 |
-1.915985 |
0.0010188 |
0.0036871 |
55968.391 |
| ENSMUSG00000064778 (Snord59a) |
0e+00 |
827709.5 |
-5.510282 |
0.0000000 |
0.0000000 |
26989.757 |
| ENSMUSG00000077191 (Snord64) |
0e+00 |
809243.9 |
-5.659871 |
0.0000000 |
0.0000000 |
13074.825 |
| ENSMUSG00000065281 (Gm24452) |
0e+00 |
793882.9 |
-3.592234 |
0.0000000 |
0.0000000 |
248493.260 |
| ENSMUSG00000064450 (Snord68) |
0e+00 |
773902.6 |
-3.873664 |
0.0000000 |
0.0000000 |
526670.399 |
| ENSMUSG00000077527 (Gm25506) |
0e+00 |
758849.2 |
-5.382228 |
0.0000000 |
0.0000000 |
282819.234 |
| ENSMUSG00000064780 (Snord95) |
0e+00 |
754801.8 |
-5.438786 |
0.0000000 |
0.0000000 |
204916.346 |
| ENSMUSG00000064612 (Gm26457) |
0e+00 |
732586.7 |
-2.693973 |
0.0000005 |
0.0000033 |
155982.017 |
| ENSMUSG00000077212 (Snord69) |
0e+00 |
691610.3 |
-4.226300 |
0.0000000 |
0.0000000 |
866766.671 |
| ENSMUSG00000077493 (Snord91a) |
0e+00 |
683841.7 |
-3.110862 |
0.0000000 |
0.0000000 |
73479.342 |
| ENSMUSG00000077625 (Snord4a) |
0e+00 |
650475.1 |
-5.631328 |
0.0000000 |
0.0000000 |
64239.224 |
| ENSMUSG00000064500 (Gm25296) |
0e+00 |
573147.5 |
-4.792521 |
0.0000000 |
0.0000000 |
375993.038 |
tRNA Read Alignment Length
Differential Expression Results (DESeq2)
Overview of DE analysis
Principal Component Analysis (PCA) of all samples
Sample distance matrix
Volcano plot showing differentially expressed genes
Features identified
Differentially expressed tRNAs
Coverage plots for all differentially expressed tRNAs
Differentially expressed ncRNAs (other than tRNAs)
Coverage plots for all differentially expressed ncRNAs
Full results for features differentially regulated in TotalRNA versus CytC_IP here:
- /home/paul/Documents/Pipelines/tsRNAsearch/../Analyses_tsRNAsearch/Mouse-Hyperosmotic-stress-Angiogenin/Data/DE_Results/DESeq2/TotalRNA_vs_CytC_IP_DESeq2-output.csv
- /home/paul/Documents/Pipelines/tsRNAsearch/../Analyses_tsRNAsearch/Mouse-Hyperosmotic-stress-Angiogenin/Data/DE_Results/DESeq2/TotalRNA_vs_CytC_IP_DESeq2-output-upregulated.csv
- /home/paul/Documents/Pipelines/tsRNAsearch/../Analyses_tsRNAsearch/Mouse-Hyperosmotic-stress-Angiogenin/Data/DE_Results/DESeq2/TotalRNA_vs_CytC_IP_DESeq2-output-downregulated.csv
Distribution Algorithm Results
Feature identified
Highest scoring tRNA fragments identified using the distribution algorithm
Full results here:
- /home/paul/Documents/Pipelines/tsRNAsearch/../Analyses_tsRNAsearch/Mouse-Hyperosmotic-stress-Angiogenin/Data/Distribution_results/TotalRNA_vs_CytC_IP_High-distribution-tsRNAs.txt
Coverage plots for all tRNAs with irregular distribution identified by the distribution algorithm
Highest scoring ncRNA fragments identified using the distribution algorithm
Full results here:
- /home/paul/Documents/Pipelines/tsRNAsearch/../Analyses_tsRNAsearch/Mouse-Hyperosmotic-stress-Angiogenin/Data/Distribution_results/TotalRNA_vs_CytC_IP_High-distribution-ncRNAs.txt
Coverage plots for all ncRNAs with irregular distribution identified by the distribution algorithm
Cleavage Algorithm Results
Features identified
Highest scoring tRNA fragments identified using the cleavage algorithm
Full results here:
- /home/paul/Documents/Pipelines/tsRNAsearch/../Analyses_tsRNAsearch/Mouse-Hyperosmotic-stress-Angiogenin/Data/Cleavage_results/TotalRNA_vs_CytC_IP_High-cleavage-tsRNAs.txt
Coverage plots for all tRNAs with irregular 5’ vs 3’ coverage identified by the cleavage algorithm
Highest scoring ncRNA fragments identified using the cleavage algorithm
Full results here:
- /home/paul/Documents/Pipelines/tsRNAsearch/../Analyses_tsRNAsearch/Mouse-Hyperosmotic-stress-Angiogenin/Data/Cleavage_results/TotalRNA_vs_CytC_IP_High-cleavage-ncRNAs.txt
Coverage plots for all ncRNAs with irregular 5’ vs 3’ coverage identified by the cleavage algorithm
More results:
tRNA fragments identified where read origin accurate only to isoacceptor level
Features ranked by combined p-value (Fisher’s method)
Other
All tRNA coverage plots can be found here:
- /home/paul/Documents/Pipelines/tsRNAsearch/../Analyses_tsRNAsearch/Mouse-Hyperosmotic-stress-Angiogenin/Plots/TotalRNA_vs_CytC_IP_Features_All-tsRNAs.pdf